DGH-GO: Clustering genes to explore the shared etiolgy of complex diseases
Asif M.
Summary
This document shows the utility of DGH-GO in exploring or studying the shared etiology of complex diseases (Autism Spectrum Disorder (ASD), Schizophrenia and Biplolar disorder).
- Data set
- source: Wang P, Zhao D, Lachman HM, Zheng D. Enriched expression of genes associated with autism spectrum disorders in human inhibitory neurons. Transl Psychiatry. 2018 Jan 10;8(1):13. doi: 10.1038/s41398-017-0058-6. PMID: 29317598; PMCID: PMC5802446.
- Only ASD, Schizophrenia and Bipolar disease were selected
- For ASD genes, an updated list of known ASD genes was obatined from SFARI gene database
Input genes
## preparing gene to GO mapping data...## preparing IC data...## [1] 3185 2## genes class
## 1 ABCB9 Schizophrenia
## 2 ACD Schizophrenia
## 3 ACTR5 Schizophrenia
## 4 ADAMTSL3 Schizophrenia
## 5 AKT3 Schizophrenia
## 6 ALDOA Schizophrenia## [1] 2594##
## ASD Bipolar Schizophrenia
## 942 1021 1222Exploratory plots of input
Dimension Reduction
Pricipal Coordinate Analysis
## [1] 2245 2247T-SNE
Clustering
Agglomerative hierarchical clustering
## Warning: `gather_()` was deprecated in tidyr 1.2.0.
## Please use `gather()` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.## cluster size ave.sil.width
## 1 1 968 -0.11
## 2 2 514 -0.24
## 3 3 763 0.49
## [1] 763 3## genes class cluster
## 5 ABCA7 ASD 3
## 13 ACD Schizophrenia 3
## 14 ACE Schizophrenia,Bipolar,ASD 3
## 23 ACTB ASD 3
## 25 ACTN4 ASD 3
## 26 ACTR5 Schizophrenia 3##
## ASD Bipolar Bipolar,ASD
## 251 135 31
## Schizophrenia Schizophrenia,ASD Schizophrenia,Bipolar
## 193 39 85
## Schizophrenia,Bipolar,ASD
## 29